SMTL ID : 8qug.1

KRAS-G12C in Complex with Compound 1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

monomer

Ligands

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.1: 21 residues within 4Å: Chain A: A.12, C.13, G.14, V.15, G.16, K.17, S.18, A.19, F.29, D.31, E.32, Y.33, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.2, MG.3 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:A.12, A:G.14, A:V.15, A:G.16, A:K.17, A:S.18, A:A.19, A:E.32, A:Y.33, A:N.117, A:K.118, A:K.118, A:A.147, A:K.148 Water bridges: A:K.17, A:S.18, A:S.18, A:E.32, A:E.32, A:Y.33, A:T.59 Salt bridges: A:K.17, A:D.120 pi-Stacking: A:F.29, A:F.29

2 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 2 residues within 4Å: Chain A: S.18 Ligands: GDP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.18, H2O.1, H2O.1, H2O.1, H2O.2 MG.3: 1 residues within 4Å: Ligands: GDP.1 No protein-ligand interaction detected (PLIP)

1 x WYU: (4S)-2-azanyl-4-methyl-4-[3-[2-[(2S)-2-methyl-1,4-diazepan-1-yl]pyrimidin-4-yl]-1,2,4-oxadiazol-5-yl]-6,7-dihydro-5H-1-benzothiophene-3-carbonitrile(Non-covalent)

WYU.4: 15 residues within 4Å: Chain A: V.10, G.61, E.63, E.64, Y.65, R.69, D.70, M.73, D.93, H.96, Y.97, Q.100, I.101, R.103, V.104 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:V.10, A:E.63, A:M.73, A:H.96, A:Y.97, A:Q.100, A:I.101 Hydrogen bonds: A:E.64, A:Y.65, A:D.70, A:D.70, A:Y.97, A:R.103 Water bridges: A:E.63, A:R.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Popow, J. et al., Targeting cancer with small molecule pan-KRAS degraders. Biorxiv (2023)

Release Date

2023-12-06

Peptides

GTPase KRas: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GTPase KRas

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